Comparison between the types for the ages and genders¶
Questions
- What are the differences between the type for the different combinations of ages and genders?
- Do we observe the same changes as globally?
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads.
preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data... preparing gene to GO mapping data... preparing IC data...
Data¶
Stats¶
| Wald padj < 0.05 | LFC > 0 (Wald padj < 0.05) | LFC < 0 (Wald padj < 0.05) | |
|---|---|---|---|
| GF VS SPF (F, 8w) | 392 | 192 | 200 |
| GF VS SPF (M, 8w) | 161 | 76 | 85 |
| GF VS SPF (F, 52w) | 738 | 316 | 422 |
| GF VS SPF (M, 52w) | 393 | 145 | 248 |
| GF VS SPF (F, 104w) | 2038 | 846 | 1192 |
| GF VS SPF (M, 104w) | 2172 | 898 | 1274 |
Differentially expressed genes¶
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”
Comparison of the numbers per ages¶
Differentially expressed genes
DEG into gene co-expression network¶
- White: up-regulated
- Black: down-regulated
| Age | F | M |
|---|---|---|
| 8w | GF vs SPF | GF vs SPF |
| 52w | GF vs SPF | GF vs SPF |
| 104w | GF vs SPF | GF vs SPF |
GO analysis¶
Biological process¶
Dot-plot with the most over-represented BP GO (20 most significant p-values for the different comparison)
Network based on description similarity
| F | M | |
|---|---|---|
| 8w | GF vs SPF | GF vs SPF |
| 52w | GF vs SPF | GF vs SPF |
| 104w | GF vs SPF | GF vs SPF |
GF VS SPF (F, 8w)
GF VS SPF (M, 8w)
GF VS SPF (F, 52w)
GF VS SPF (M, 52w)
GF VS SPF (F, 104w)
GF VS SPF (M, 104w)
Cellular components¶
Dot-plot with the most over-represented CC GO (20 most significant p-values for the different comparison)
Warning message: “Removed 7 rows containing missing values (geom_point).”
Molecular functions¶
Dot-plot with the most over-represented MF GO (20 most significant p-values for the different comparison)
Warning message: “Removed 7 rows containing missing values (geom_point).”
KEGG pathways¶
[1] "Note: 11 of 4057 unique input IDs unmapped." [1] "Note: 11 of 4057 unique input IDs unmapped."
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limit_output extension: Maximum message size of 10000 exceeded with 10090 characters
Pathway graphs available at ../results/dge/type-effect/type_gender_age/over_repr_kegg/
[1] "Note: 11 of 4057 unique input IDs unmapped."
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[1] "Note: 11 of 4057 unique input IDs unmapped."
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limit_output extension: Maximum message size of 10000 exceeded with 10090 characters
Pathway graphs available at ../results/dge/type-effect/type_gender_age/under_repr_kegg/
Comparison with Erny results¶
Protocol: 2 months old female mices (GF vs SPF)
Raw comparison of the results¶
Detailed comparison¶
- Checking the correlation between the counts of Erny and our counts
- Re-running a DGE analysis on the Erny's raw counts